AMBER Archive (2008)

Subject: RE: AMBER: ptraj problem with centering in the box

From: Ross Walker (
Date: Wed Jul 02 2008 - 10:31:51 CDT

Hi Hannes,

Have you run a constant pressure (NPT) simulation to equilibrate the
pressure? Leap by default sets the box size too large, to avoid steric
clashes, and so if you do not equilibrate pressure you end up with the
density too low and vacuum bubbles will form. In your case though the image
looks like what I would expect if you did some kind of centering of the
inpcrd file created by leap rather than after a reasonable length MD
simulation. Which frame of MD are you showing here? If this is the first
frame then this at least makes some sense. What does it look like at the end
of the trajectory file?

You could try opening the unimaged trajectory in VMD and having it display
the periodic boxes and see if the gaps are there - It is under graphical
representations -> periodic if I remember correctly.

Beyond that I think we will need more details to be able to help some more.

All the best

> -----Original Message-----
> From: [] On Behalf
> Of Hannes Wallnoefer
> Sent: Wednesday, July 02, 2008 7:01 AM
> To:
> Subject: AMBER: ptraj problem with centering in the box
> Hello Amber-users,
> I have a problem when i want to get my protein back into the box after the
> MD. I
> tried the following ptraj script:
> trajin trajectory files
> center origin :1-234
> image origin center
> trajout output trajectory
> 1-234 are the residues of my protein.
> When i look at the output trajectory there is a gap in the box. This gap
> moves
> during the trajectory. It seems as if there is a small slide of vacuum
> between
> all of the periodic boxes. I added a screenshot of the last snapshot.
> Has anybody ever seen that? Are there suggestions how to get rid of that
> or what
> has gone wrong?
> Best regards,
> Hannes

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